ERR13110290 · Gut microbiome

BACMIX_minion_v1_9_20230623_zymo_magbead_NZ3

complete

Gut analysis is paused. Unfinished samples are not negative results. This is a mixed-host collection, not a curated human-only cohort.

Open interactive sample report

Taxonomic abundances

Species	Genus	Abundance (%)
Staphylococcus aureus	Staphylococcus	16.2964
Escherichia coli	Escherichia	13.7811
Salmonella enterica	Salmonella	12.8596
Listeria monocytogenes	Listeria	11.2907
Bacillus amyloliquefaciens	Bacillus	7.3146
Bacillus velezensis	Bacillus	6.7216
Limosilactobacillus fermentum	Limosilactobacillus	4.7855
Enterococcus faecium	Enterococcus	4.1695
Bacillus subtilis	Bacillus	3.9107
Enterococcus faecalis	Enterococcus	3.5611
Pseudomonas aeruginosa	Pseudomonas	1.5187
Listeria ivanovii	Listeria	1.3667
Enterococcus hirae	Enterococcus	1.1029
Staphylococcus pseudintermedius	Staphylococcus	1.0150
Shigella sonnei	Shigella	0.7836
Shigella dysenteriae	Shigella	0.6765
Listeria welshimeri	Listeria	0.6610
Lactobacillus delbrueckii	Lactobacillus	0.6237
Bacillus cereus	Bacillus	0.5946
Bacillus licheniformis	Bacillus	0.4950
Escherichia fergusonii	Escherichia	0.4479
Bacillus thuringiensis	Bacillus	0.4378
Limosilactobacillus mucosae	Limosilactobacillus	0.4337
Listeria innocua	Listeria	0.4194
Limosilactobacillus oris	Limosilactobacillus	0.4005
Lactobacillus psittaci	Lactobacillus	0.3807
Limosilactobacillus gorillae	Limosilactobacillus	0.3409
Listeria grayi	Listeria	0.3378
Enterococcus avium	Enterococcus	0.3191
Staphylococcus argensis	Staphylococcus	0.2909
Enterococcus columbae	Enterococcus	0.2735
Pseudomonas frederiksbergensis	Pseudomonas	0.2657
Staphylococcus lugdunensis	Staphylococcus	0.2585
Bacillus halotolerans	Bacillus	0.2581
Limosilactobacillus reuteri	Limosilactobacillus	0.2278
Listeria seeligeri	Listeria	0.2106
Listeria cornellensis	Listeria	0.2062
Bacillus pumilus	Bacillus	0.1894
Staphylococcus haemolyticus	Staphylococcus	0.1727
Bacillus nakamurai	Bacillus	0.1452
Enterococcus saccharolyticus	Enterococcus	0.1323
Staphylococcus sciuri	Staphylococcus	0.1137
Enterococcus canis	Enterococcus	0.1050
Staphylococcus saprophyticus	Staphylococcus	0.1042

Saved public metadata

{
  "run_accession": "ERR13110290",
  "study_accession": "PRJEB75753",
  "sample_accession": "SAMEA115615489",
  "instrument_platform": "OXFORD_NANOPORE",
  "instrument_model": "MinION",
  "library_strategy": "AMPLICON",
  "library_source": "METAGENOMIC",
  "library_selection": "PCR",
  "read_count": "736770",
  "base_count": "1118360006",
  "fastq_bytes": "1058712239",
  "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR131/090/ERR13110290/ERR13110290.fastq.gz",
  "sample_title": "BACMIX_minion_v1_9_20230623_zymo_magbead_NZ3",
  "scientific_name": "gut metagenome"
}

Public files

ERR13110290.fastq.gz

Analysis provenance

{
  "marker": "16S",
  "pipeline": "Archaions v18.8",
  "cohort": "Gut, mixed hosts; not curated as a human-only cohort",
  "execution_state": "paused_by_user",
  "sample_state": "complete",
  "read_sampling": "First available reads; not random subsampling",
  "input_sha256": "88661eabc52745fc841de37946026a768d385963e65893eb9d180c67ceb5ce5c",
  "length_window_bp": [
    1200,
    2000
  ],
  "median_read_length": 1588.0,
  "quality_scores": "No measured quality scores in fetched FASTA",
  "classifier_stats": {
    "marker": "16s",
    "pipeline": "v18.8",
    "gpu": "RTX-PRO-6000",
    "input_path": "volume-fastq-gz",
    "reads_in": 30000,
    "reads_skipped": 4720,
    "elapsed_seconds": 9.779721319999993,
    "reads_submitted": 30000,
    "reads_after_filter": 30000,
    "adapter_scan": {
      "sampled": 200,
      "matched": 18,
      "fraction": 0.09,
      "adapters_found": {
        "27F": 18
      },
      "should_trim": true
    },
    "porechop_ran": false,
    "porechop_reason": "fast-path: no adapter trimming required"
  },
  "metadata_coverage": "Saved ENA run fields only. BioSample attributes, study abstracts and file MD5s have not been fetched for this panel."
}